use strict;
use warnings;

use Data::Dumper;

open my $in1FH, q{<}, \ <<END_File1 or die qq{open: < "File1.txt": $!\n};
155369268 5 * 
169212695 7 *
175387629 127 *
END_File1

my %positions = ();
while( <$in1FH> )
{
    my( $key, $posn, $locn ) = split;
    $positions{ $key } = {
       position => $posn,
       location => $locn,
       };
}
close $in1FH or die qq{close: < "File1.txt": $!\n};

print Data::Dumper->Dumpxs( [ \ %positions ], [ qw{ *positions } ] );

open my $in2FH, q{<}, \ <<END_File2 or die qq{open: < "File2.txt": $!\n};
>gi|155369268|ref|NM_001100917.1| After all
AAACAATGTCGATTCTATGATGCGAACGCAGCATTTCAGGGACTGGATGAGGAGCTTACGGTTTTTTACT
ACAGAATCATCAATATCTTGGAAGAAAAAGAATGTTAAGAAATAACAAAACAATAATTATTAAGTACTTT
>gi|169212695|ref|XM_001716884.1| Its the code 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
>gi|175387629|ref|PM_001716884.1| Its the code again
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
AAGCTTTCTAAATGGCCCCGGGGCTTTGTCATTCAAGGGTGTGCCCAAGCCATTGTCTTGAAGAGGGGGT
CGGGGCTTTTCAAGGGTCATTGTGCCCAAG
>gi|192669295|ref|XM_001716884.1| Its the code 
AGACAAGCTTGTCCTGATGTTCCTTGCCCTGGCAGATGTTCAGGACCTTCCTTTGATTCAACCCCTCCAC
CTAAATGGCCCAAGCTTTCGGGGCTGTCATTGTCTGTTTGTCATTCAAGGGCCCAAGCTGAAGAGGGGGT
END_File2
#        1        2          3         4         5         6         7
#234567890123456789012345678901234567890123456789012345678901234567890

my $rsFile2out = \ do{ my $dummy };
open my $outFH, q{>}, $rsFile2out
   or die qq{open: > "File2out.txt": $!\n};

my $record = <$in2FH>;
while( <$in2FH> )
{
    if( m{^>gi} )
    {
        processRecord( $record );
        $record = $_;
    }
    else
    {
        $record .= $_;
    }
}
processRecord( $record );

close $in2FH or die qq{close: < "File2.txt": $!\n};
close $outFH or die qq{close: > "File2out.txt": $!\n};

print ${ $rsFile2out };

sub processRecord
{
    my $record = shift;
    my $key = ( split m{\|}, $record )[ 1 ];
    if( exists $positions{ $key } )
    {
        my( $header, @data ) = split m{\n}, $record;
        my $dataStr = join q{}, @data;
        substr
           $dataStr,
           $positions{ $key }->{ position } - 1,
           1,
           $positions{ $key }->{ location };
        print $outFH join qq{\n},
           $header,
           unpack( q{(a70)*}, $dataStr ),
           q{};
    }
    else
    {
        print $outFH $record;
    }
    
    return;
}